Mobile traffic in cellular based networks is increasing exponentially, mainly due to the use of data intensive services like video. Network operators are urged to explore new technologies in order to enhance the capacity, data rates and maximizing the utilization of available spectrum resources. One effective way to cope with these demands is to reduce the cell-size by deploying small-cells along the coverage area of the current macro-cell system. In this paper, we consider the uplink of heterogeneous network with a number of small-cells coexist with a macro-cell under the same frequency band. To deal with inter-tier/system interference, we combine signal alignment (SA) based precoding at the small-cell transmitters in conjunction with physical network coding (PNC) at the macro-receiver. The joint design of SA and PNC provides higher system degrees of freedom (DoF), than the case where only PNC or interference alignment (IA) is employed individually. The results show that the proposed scheme is robust to inter-tier/system interference while allowing to increase the overall data rate, by serving more users, as compared with the IA based methods.